[gmx-users] autocorrelation time of dVpot/dlambda?

[Michael Shirts]

> I am doing free energy calculation in Gromacs and want to get an error
> estimate of my results. Is it possible to compute the autocorrelation time
> of dVpot/dlambda in Gromacs using a certain length of trajectory such as 10
> ns? Thanks a lot

The amount of simulation time required to compute the autocorrelation
time of dVpot/dlambda will depend on the timescale of the system.  You
should be able to use g_analyze to analyze the energy.xvg output, and
get an autocorrelation time.  If your simulation time is 50x longer
than the autocorrelation time, then you are very likely converged.
However, if there are very long correlation times, you still might not
have captured all of the time dependent variations in  Vpot/dlambda.